‘Fold it’- protein puzzles for everyone.

This blog post is a re-blog of the “‘Fold it’- protein puzzles for everyone” which was originally posted during 2013 on another blog site, which is no longer operational. 

Fold it is an invitation to participate in science everyday. You don’t need to be a biologist or even a scientist to participate in this ground breaking research. All you need is to enjoy puzzles and games.
What started as a way for researchers from the University of Washington to access the hard drive of home computers to help generate more time solving the possible protein folding configurations, has now developed into a very successful, crowd sourced science research project. You can read more about the history of the project here: http://fold.it/portal/info/about, and about some of it’s successes here: http://www.scientificamerican.com/citizen-science/project.cfm?id=foldit-protein-exploration-puzzle,
http://www.scientificamerican.com/article.cfm?id=foldit-gamers-solve-riddle and in a journal here: http://www.nature.com/nature/journal/v466/n7307/full/nature09304.html.
If you happen to be a biologist, you will be aware that proteins are one of the foundation molecules that make basic cell function possible. Peptides (sub units of proteins) are joined in various ways, following the instructions from RNA. There are many combinations of peptides which lead to different proteins and a range of different functions within cells and organisms. Now, if you happen to be a Biology teacher, Unit 3 and 4 of VCE Biology require students to develop a working knowledge of proteins, their structure and function. One approach to teaching such ‘abstract’ concepts is to use modelling.
There are many modelling tools available to help students conceptualise the structure and function of proteins, these include Toobers: http://www.umass.edu/molvis/toobers/, Cn3D:http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml, bio-molecular 3D explorer: http://www.umass.edu/molvis/bme3d/materials/explore.html, and many resources at the Protein Data Bank (PDB) including the archive of molecule of the month: http://www.pdb.org/pdb/motm.do;jsessionid=D608F408EC87F4494ED671924DD998B8. Fold-it is another tool we can tap into.
Fold-it provides an opportunity for students (and teachers) to be directly involved in ground breaking research. In addition this game may help to develop a better understanding of the rules and nature of protein folding. It is a wonderful example of promoting the use of real life applications within, and beyond, the classroom. It is also a great way of promoting skills like problem solving and collaboration. So, will you and your students come and play?
Until next time,
Fiona T

The PhD and side quests

A while ago I read a tweet http://researchblog.iclon.nl/phd-side-quests-teaching/  likening various distractions (like teaching) to a side quest in a multiplayer online game. Even though I’m part time on my PhD and full time teaching, I find this tweet still resonated with me. At present I feel very stretched- full time academic teaching load, additional (short term) administrative role, part time PhD student, and Mum- it’s always busy and every minute is precious in each role. When I do have blocked time for my PhD analysis and writing I feel like if I am not writing actual words into a chapter that somehow I am not working effectively enough, then I realised I had to change my personal PhD narrative if I was going to do this to the best of my ability. Let me explain…

A few weeks ago I was up to day 5 of what would be a 2 week lack of motivation for my studies. I felt tired, overwhelmed and frustrated that this sacred writing time was being wasted while I looked up new references, read over old data and tried to re-envision my literature review while writing a data chapter. I was thinking about changing the chapter structure of the thesis to follow themes rather than data sets, this was going to be a huge shift. There was textas, A3 paper, muttering and scribbling. Mendeley was getting a workout as I uploaded and annotated more articles. I was busy, but didn’t feel like I was making progress visible to anyone else. I briefly considered walking away from the PhD- but am so close to being finished I know I would regret it. By day 5 I realised the truth- I was caught up in a side quest! As my thesis links to games, learning and aspects of motivation, I realised I was living the kinds of scenarios I had been researching for the last few years; what motivates a person to push past this point, where it all seems too hard to manage? I looked to my data, and my own personal side quests- my craft and other blogs. If you follow these blogs : one mad tatter and My WISE Dolls, you may notice that my whole life in recent years is chipping away at various goals over a longer period of time. It isn’t about being motivated to complete a project in one day, and my thesis is another such project.  I realised that I needed to be my own advocate, and so I gave myself permission to just be- to leave the actual writing of my chapter for a few days and go on a side quest of reading and thinking. This took me another week or so, but after this time I felt again in a position to edit and write some more. Last week I sent the finished chapter to my advisory group for feedback- and it felt like an epic win!

The side quest was an important part of the journey, of narrowing down the new articles to those that could be used to support my data and the unfolding story in my thesis. The ‘re-envisioning’ of the thesis was also deemed a side quest, confirming that the chapter structure I have drafted over the last 2 years will work better for my thesis than the one in my clouded mind a few weeks ago. While these two processes didn’t make a visible difference to my writing and work so far, they have helped me to think through my options and make firm choices on the direction of my thesis, and so this clarity of mind makes the side quest worthwhile in my opinion. The PhD is as much about the thinking, pondering and analysing as it is about the written submission. I need to wander down some of the pathways to realise they are dead ends. And, even if I don’t feel like writing, there are lots of tasks to to that will contribute in different ways to the completed submission.

Some side quests might be setting up fonts, highlighting relevant data, creating images and labelling figures- they are important small tasks that support the end goal. These are what help build the thesis from the ground up, and no one else can do it for me; I have to own the whole quest, not just the fun bits 🙂 I need to remind myself of the work I have been doing towards this since 2011, for all intents and purposes I have done the hard yards; the planning, considering methodological protocols, completing ethics for university and education departments, approaching schools, and building relationships with principals, teachers and students in order to generate data on site. I have the conceptual framework in place and have identified the gaps in the research my study seeks to contribute to. I have come a long way in my writing and thinking, been supported by a fabulous team of family, friends and colleagues and really love my topic. With less than a year to go until submission, I need to remind myself “I’ve got this!” 🙂

I still need to recognise that some side quests are time sinks, and wont be helpful in the bigger scheme of things for the PhD goal. For example, my WISE Dolls site is exciting and will be great, but it doesn’t need to be the focus of my energy this year, it will be waiting for me to pick it up again next year. The same with some of my tatting design ideas and goals, these too will wait until I am on the other side of thesis submission. In recognising these as alternate side quests I can more easily make a clear decision to refocus my precious PhD time to the side quests really need my focus here and now.

So, it seems the side quest metaphor works for me, here is a link to a paper about such metaphors for PhD work (McCulloch, 2013)  http://w3.unisa.edu.au/researcheducation/contact/documents/mcculloch-2013.pdf
or perhaps the Map for the PhD student graphic (MGSE, 2012) http://education.unimelb.edu.au/__data/assets/pdf_file/0011/621929/Map_for_the_PhD_Student.pdf might resonate with you. Whichever you decide, make sure you can identify for yourself what will be a productive use of your time, and keep your eye on the prize- that PhD 🙂
Until next time, happy questing
Fiona T
NB: It was also confirmed by my Wonderful Husband that this post is ironic- it was a side quest too. Now I have blogged it, it is completed [Achievement unlocked: 1084 words posted on PhD Blog] and I guess it’s back to the data for me 🙂

Tinker tailor: up-cycling, problem solving and learning

This past week I was lucky enough to be able to run a ‘maker movement’ workshop with my students (who are adults training to be teachers 🙂 ). My inspiration came from the following sources, as indicated below in my blurb for the workshop:

The maker movement is gathering traction in the US and internationally: https://www.techopedia.com/definition/28408/maker-movement. It recognises the need to have young people explore technology by taking it apart, finding out how it works and redesigning the technology to make some thing new. There are strong Science, Technology, Engineering, Art and Math (STEAM) links here that we can harness in schools, either as part of formal curriculum, or as an extension/engagement opportunity. We will be deconstructing McDonalds toys (which can’t go to landfill) and up-cycling them to make artistic posters OR redesigning them to make a new toy/item- It is up to you. Examples: http://www.telegraph.co.uk/culture/art/art-news/7675915/Artist-builds-sculptures-from-circuit-boards.htmlhttp://www.sodapopgirl.net/art/disassembly/ and http://www.toddmclellan.com/commercial#5 .

The purpose of the workshop was for them to experience first hand the wide educational potential of an open ended invitation to up-cycle some old McDonald’s toys. Why McDonald’s toys? When my son, Little Tacker (LT) was younger we would have McDonald’s as a semi-regular treat, and very quickly accrued a pile of plastic single purpose toys. When he was about 5 I cleared out his room and found we had heaps, and the problem became how to dispose of them. The toys are plastic and often have batteries in them, meaning we can’t put them into the plastic recycling bins or landfill. So I finally had an opportunity to use them with a class and see how creative we could be.

Unfortunately many of these toys have (what I now know to be) Security screws that need a specialist triangular bit to undo them….and I had bought a few sets of small Phillip’s head and flat head screw drivers for my students to use- Whoops! Fortunately this was only a hiccup for a short time in the workshop and my students were able to problem solve and figure out different ways of opening the toys and re-purposing them. Below are some pictures of the ‘end products’.

Inside a clock work smurfThis was a clockwork Smurf toy- it ‘laid down’ and rotated on a ball attached to it’s feet and would intermittently turn to balance on it’s elbows, then go back to rotating on the ball. After much perseverance the student with this toy was able to break away part of the body and remove the cogs that performed the motion.  The two cogs had different arrangements of teeth which gave rise to the ‘intermittent’ movements we observed int he working toy. This lead to a small group discussion about one of the earliest forms of programming being the Jacquard Loom. A very interesting discussion that created curiosity and a few email discussions after the session too. Inside a pop up toy smurf

This student had a ‘pop-up’ present Smurf, and was able to reassemble her toy as a 3D item to display the inner workings.

Up cycled mobile

This student made a ‘superhero mobile’ – pictured flying over Melbourne 🙂 Upcycled ringA couple of students up-cycled their toys into Jewellery- Ninja Turtle rings anyone?

This workshop was great fun and highlighted an opportunity to engage students in a STEAM (Science, Technology, Engineering, Art, Math) experience. It also created a high level of cognitive engagement and curiosity in the group- me included! I have now found the screw drivers we need on ebay – so will source some before I run this workshop again next year. I would like to thank my students for agreeing to let me use photos of their creations and share their stories here too.

Until next time- happy tinkering.

Fiona T






Healing blade- a biology card game.

This story started in 2011, when I first read about the “Healing blade card game” From Nerdcore in this blog: https://drottematic.wordpress.com/2011/08/11/review-healing-blade-the-infectious-disease-card-battle/.    I began to search for this game, knowing it would probably be too advanced for the VCE (Victorian Certificate of Education- Year 12) course I wanted to use it for. Healing blade was developed for Medical students to use as a learning tool- and this is what intrigued me the most, the information within this game wouldn’t be “dumbed down” or incorrect. To me, accuracy is a very important aspect of any game I would want to use as a learning tool.

Unfortunately, the game had a small initial print run and it took me quite a while to find out about the kickstarter movement and track down the print and play version. Late last year I received the newest version of the downloadable file. I was impressed with the quality of the card fronts and really wanted to print these out on card stock for my classes to work with. The months flew by, and the printing of the cards was pushed on down the priority list. Then the sudden realisation that I need the cards for my class this week hit me! So, I have compromised and printed out my card set on a normal photocopy paper. I spent a couple of hours yesterday cutting up the paper cards and backs and sliding them into plastic card holders (Thanks MindGames on Swanston St for your help in sizing the right ones).

Sometimes the work of teaching is ‘making’ the resources 🙂

Healing blade pic for blog

Now the game is ready to play.

Along with 6 other Biology based games, Healing blade will be considered by my students this week, and critiqued as a possible classroom tool.

I hope, in the coming weeks, that I will blog about our impressions of each of the 7 games we will critique, so stay tuned 🙂 (or link the RSS feed to your email, so you don’t miss out!)

Until next time,

Fiona T


Re-blog: The Happy PhD Zone: How To Maintain A Work-Life Balance In Academia – Next Scientist

I recently read this post over at Happy PhD zone, and it made me laugh, and think about my priorities at the moment too. I am trying to balance my time on weekends to make sure I recharge and spend time with my beautiful family. The PhD and a full time teaching load make for very busy week days. So, this blog is worth a look 🙂

The Happy PhD Zone: How To Maintain A Work-Life Balance In Academia – Next Scientist.

Until next time,

Fiona T

Re-Blog: 7 Smart Ways To Use Evernote For Research As A PhD – Next Scientist

OK- I still Love, Love, Love Evernote. It is one of my 3 technology saviours for my PhD and academic work (the other two are Dropbox and Mendeley) Here is a blog I read a while ago with some great tips for using Evernote to better organise your research. They had me very early on with the comparison to a ‘swiss army knife’… read on and enjoy 🙂

7 Smart Ways To Use Evernote For Research As A PhD – Next Scientist.

Until next time,

Fiona T

Games and toys that promote creativity and thinking (Part 6) Review of Goldiblox and the spinning machine

Hi to all my followers- I’m sorry to say that I have neglected this blog for a little while. It has taken one of my new students this year to prompt me to write again, so I will try to write fortnightly posts about ICT study tools, games, toys and learning. Welcome back 🙂

Here is part 6 of a series of posts looking at commercially available* toys and games that can promote creativity and thinking in our kids, at home and at school. When I refer to creativity and thinking, I mean that children (and adults) have the opportunity to approach these toys in a variety of ways, not necessarily just the way described on the box. Creativity may involve changing rules, or allow a ‘free playing’ imaginative space for children to explore. Thinking, and expectations around thinking, will vary depending on the child and adult playing, for example it may be thinking about turn taking, sharing, language development, rule making or even just having a fun and relaxing space to talk in.

This week I am looking at “Goldi Blox” story/game that can support creativity and thinking through play. I had seen this in the stores a few times and wondered if it would be a suitable present. In a recent discussion with a colleague, I found that she had the story/game and used it as part of her teaching- so I asked to borrow it.


It comes with a story that takes you and your child through building the spinning machine- and is an introduction to belt drives, as an engineering concept. The aim is to make a machine that will spin all of the characters in the book- they are figurines in the box. There are also extra challenges in the book, to continue playing with.The book uses funny rhymes to engage the imagination too.

2015-03-20 16.48.07For the age range stated it is appropriate as a learning object.  I feel that adding just a few cogs and wheels as extra pieces here would serve as a strong extension to the belt drive ideas. This would open up a range of open ended play opportunities and begin to explore gear ratios to get the character figurines to spin at different speeds. I would probably purchase this for a 4 to 5 year old as a present.

There are other a few other games, like ‘mouse trap’ where machines are set up as part of the game, but this is the first one I have seen for a younger age group and with a story to accompany it. I wonder if you have seen any other such items available. If you have, please share them below in the comments 🙂

Until next time

Fiona T

*All opinions are my own, and are unsolicited. I personally purchase all items reviewed on this blog and have received no payment from any supplier for promoting their goods. I am a student/teacher/academic and have no personal business affiliation or business motive on this blog. Opinions expressed are my own, and are not necessarily endorsed by my employer.

Games and toys that promote creativity and thinking (Part 5)

Here is part 5 of a series of posts looking at commercially available* toys and games that can promote creativity and thinking in our kids, at home and at school. When I refer to creativity and thinking, I mean that children (and adults) have the opportunity to approach these toys in a variety of ways, not necessarily just the way described on the box. Creativity may involve changing rules, or allow a ‘free playing’ imaginative space for children to explore. Thinking, and expectations around thinking, will vary depending on the child and adult playing, for example it may be thinking about turn taking, sharing, language development, rule making or even just having a fun and relaxing space to talk in.

This week I am looking at Lego (and similar building style toys, including mega blocks, mecanno, and even the digital space of minecraft) as a toy that can support creativity through play.

The photos above are from a game of  ‘Lego creationary’ (think: pictionary with lego). This game has players make particular items and the other players need to guess the item made – lots of creative fun, competition and open ended play. The other Lego games also encourage exploratory play – games like Heroica, Minotaur, and Lego city police all have starting points for game play and set up, and as you play them more you can adapt the game board and rules to change the challenge level.

Aside from the more recent Lego games, Lego itself is a great open ended play tool. It does come in sets, with instructions to build the item on the box, and then once this is done and played with, the real fun begins. Children (and yes, adults too) can work together to build infinite objects. Today this is classified as a ‘sandbox game/space’ – an opportunity for open ended play where the child can be in charge.  Mecanno is very similar, but uses tools, nuts and bolts  to build machines.  Minecraft is a digital space that now fits this definition  – for a review of this please see: http://appsforaussiekids.blogspot.com.au/2014/06/minecraft-for-parents-part-2-of.html .   After getting used to the controls in Minecraft you can play and build whatever you want.  Playing with any of these alongside and with your child can lead to lots of fun, and learning for both of you 🙂 Setting challenges to ‘build’ – like building your house in Minecraft – can be interesting to collaborate on, as there are lots of problem solving opportunities that present themselves as you work though the challenge together.

So, what ‘sandbox games/spaces’ do you like? How else might you incorporate this style of game/toy to extend opportunities for develop thinking skills? Perhaps you would like to share a picture of your families collaboration in one of these spaces? Please share in the comments : )

Until next time

Fiona T


*All opinions are my own, and are unsolicited. I personally purchase all items reviewed on this blog and have received no payment from any supplier for promoting their goods. I am a student/teacher/academic and have no personal business affiliation or business motive on this blog. Opinions expressed are my own, and are not necessarily endorsed by my employer.

Dropbox update – MyPaperless PhD

Just a quick post today-

After thinking that I wasn’t saving to dropbox properly at work, I found the real problem was not closing the windows/programs I was working with on my laptop. I was inadvertently overwriting the work I did at work when I would open my laptop later in the day. Dropbox, being uber efficient, was updating the files fine 🙂 . I did find, by using opening my dropbox account on the web, that you can search previous versions of folders and files and re-instate the one you need- thanks dropbox.

I also recently upgraded my dropbox storage and began paying for this extra space- imagine my surprise when Dropbox announced last week they were upgrading all pro- storage to 1TB for no extra charge! Very happy with that 🙂

Until next time

Fiona T

Digital tools- Rocking my world

Last weekend I had the pleasure of attending a post-graduate research conference run by my Graduate School. It ran over 2 days, and I attended one of them. The day was fabulous and inspiring. We started with my fellow ‘shut up and writer’ and I running a modified ‘Shut up and Write’ session, so those who can’t normally make our weekday sessions could get a feel for how this works. We also hoped that they would perhaps join us during semester, or begin using this method on their own. I got to make a good start on a conference paper, so I was very happy 🙂 The feel from the others was very positive too. We also had some discussion groups based around our stage of study, and workshops on what examiners are looking for and publications for different audiences. All interesting and insightful.

The session that rocked my little world was the ‘taming your thesis with technology’ session. I have been looking for this session for the last few years.  The workshop leader was inspirational, and showed us a glimpse of the true power of the word-processing tools we have as standard installations on our computers. Setting up styles within documents, and using these to easily format tables of contents, figures and tables…let me just say it was an enthralling 2 hours. I have been generating small scale reports for my key stakeholders, and I know that even with these small documents, the tips from this workshop will save me much time and angst…I can only imagine how much time and angst will be saved when I put the sections of my thesis together 🙂  I still recall the nightmare of pulling my Masters’ Thesis together – reprinting and formatting to make sure the table of contents matched the actual headings and page locations, not to mention when I had to move a figure or section eeek…. I am very much looking forward to NOT having to do that again 🙂

By Renee and sourced from: http://kpc.am/11bBpds

By Renee and sourced from: http://kpc.am/11bBpds

Along with Mendeley, Evernote and dropbox, it seems my word processor will be another reliable digital tool for my studies.

I wonder, what tip, trick or tool is saving you time and angst? Please feel free to share in the comments below, or on the facebook page 🙂

Until next time

Fiona T


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